# HG changeset patch # User greg # Date 1509713567 14400 # Node ID 94f6b3e28c36cc543e3cf560c5bf91e8625c49bb Uploaded diff -r 000000000000 -r 94f6b3e28c36 dmri.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dmri.py Fri Nov 03 08:52:47 2017 -0400 @@ -0,0 +1,51 @@ +#!/usr/bin/env python +import argparse +import os +import nibabel +import shutil + +from dipy.data import fetch_sherbrooke_3shell + +parser = argparse.ArgumentParser() +parser.add_argument('--input', dest='input', help='Input dataset') +parser.add_argument('--output', dest='output', help='Output dataset') + +args = parser.parse_args() + +def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): + source_directory = os.path.abspath(source_dir) + destination_directory = os.path.abspath(destination_dir) + if not os.path.isdir(destination_directory): + os.makedirs(destination_directory) + for dir_entry in os.listdir(source_directory): + source_entry = os.path.join(source_directory, dir_entry) + if copy: + shutil.copy(source_entry, destination_directory) + else: + shutil.move(source_entry, destination_directory) + if remove_source_dir: + os.rmdir(source_directory) + +input_dir = 'input_dir' +# Get input data. +fetch_sherbrooke_3shell() +# MNove inputs to working directory. +move_directory_files('/home/greg/.dipy', input_dir) +fdwi = join(input_dir, 'HARDI193.nii.gz') +fbval = join(input_dir, 'HARDI193.bval') +fbvec = join(input_dir, 'HARDI193.bvec') +# Load the dMRI datasets. +img = nibabel.load(fdwi) +data = img.get_data() +# data is a 4D array where the first 3 dimensions are the i, j, +# k voxel coordinates and the last dimension is the number of +# non-weighted (S0s) and diffusion-weighted volumes. +# Visualize the results using matplotlib. +axial_middle = data.shape[2] // 2 +plt.figure('Showing the datasets') +plt.subplot(1, 2, 1).set_axis_off() +plt.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower') +plt.subplot(1, 2, 2).set_axis_off() +plt.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower') +plt.show() +plt.savefig(args.output, bbox_inches='tight') diff -r 000000000000 -r 94f6b3e28c36 dmri.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dmri.xml Fri Nov 03 08:52:47 2017 -0400 @@ -0,0 +1,33 @@ + + real-time object detection + + dipy + nibabel + matplotlib + + + + + + + + + + + + + +**What it does** + +----- + +**Options** + + + + +